Compositions comprising bacterial strains

Abstract

The invention provides compositions comprising bacterial strains for treating and preventing inflammatory and autoimmune diseases.

The invention claimed is: 
     
       1. A method of reducing inflammation caused by Th17 differentiation in a subject, comprising orally administering to the subject a pharmaceutical composition that comprises
 a therapeutically effective amount of a bacteria strain of genus  Bifidobacterium;    
 wherein the  Bifidobacterium  bacteria strain is lyophilized; 
 wherein the  Bifidobacterium  bacteria strain is positive for fermentation of raffinose as determined by an Analytical Profile Index test comprising:
 (a) contacting a suspension of the  Bifidobacterium  bacteria strain with a Rapid ID 32A strip at 37° C. for at least 4 hours; 
 (b) contacting the suspension with a development reagent comprising FastBlue for at least 5 minutes; and 
 (c) measuring a color of the suspension; 
 
 wherein the therapeutically effective amount comprises from about 1×10 6  to about 1×10 11  CFU/g of the  Bifidobacterium  bacteria strain with respect to a total weight of the pharmaceutical composition; and 
 wherein the administering of the therapeutically effective amount of the  Bifidobacterium bacteria strain results in a reduction of inflammation caused by Th17 differentiation. 
 
     
     
       2. The method of  claim 1 , wherein a bacterial cell of the  Bifidobacterium bacteria strain binds to a human cell to a lesser extent than a bacterial cell of  Bifidobacterium breve  strain JCM 7017 binds to a corresponding human cell, as determined by an in vitro assay comprising comparing a measurement of an optical density. 
     
     
       3. The method of  claim 1 , wherein the administering of the therapeutically effective amount of the pharmaceutical composition to the subject decreases an amount of IL-17A, IL-17B, IL-17C, IL-17D, IL-17E, IL-17F, IFN-y, IL-10, IL-6, or TNFa; relative to an amount prior to the administering. 
     
     
       4. A method of reducing inflammation caused by Th17 differentiation in a subject, comprising orally administering to the subject a pharmaceutical composition that comprises
 a therapeutically effective amount of a bacteria strain of species  Bifidobacterium breve , wherein the  Bifidobacterium breve  bacteria strain is lyophilized; 
 wherein the  Bifidobacterium breve  bacteria strain is positive for fermentation of raffinose as determined by an Analytical Profile Index test comprising:
 (a) contacting a suspension of the  Bifidobacterium breve  bacteria strain with a Rapid ID 32A strip at 37° C. for at least 4 hours; 
 (b) contacting the suspension with a development reagent comprising FastBlue for at least 5 minutes; and 
 (c) measuring a color of the suspension; 
 
 wherein the therapeutically effective amount comprises from about 1×10 6  to about 1×10 11  CFU/g of the  Bifidobacterium  breve bacteria strain with respect to a total weight of the pharmaceutical composition; and wherein the administering of the therapeutically effective amount of the  Bifidobacterium breve  bacteria strain results in a reduction of inflammation caused by Th17 differentiation. 
 
     
     
       5. The method of  claim 1 , wherein the  Bifidobacterium bacteria  strain is a  Bifidobacterium  bacteria strain deposited under accession number NCIMB 42380. 
     
     
       6. The method of  claim 1 , wherein the pharmaceutical composition further comprises a pharmaceutically acceptable excipient, diluent, or carrier. 
     
     
       7. The method of  claim 1 , wherein the  Bifidobacterium  bacteria strain produces an amount of an exopolysaccharide on a surface of a bacterial cell of the  Bifidobacterium  bacteria strain that is greater than an amount of the same exopolysaccharide produced by a bacterial cell of  Bifidobacterium breve  strain JCM 7017 as determined by an in vitro assay comprising:
 a. binding of the exopolysaccharide to Congo Red; and 
 b. measuring a light absorbance of the Congo Red bound to the exopolysaccharide for the bacterial cell of the  Bifidobacterium  bacteria strain and the bacterial cell of the  Bifidobacterium breve  strain JCM 7017; and 
 c. comparing the light absorbance of the Congo Red bound to the bacterial cell of the  Bifidobacterium  bacteria strain and the bacteria bacterial cell of the  Bifidobacterium breve  strain JCM 7017. 
 
     
     
       8. The method of  claim 1 , wherein the subject has a condition that comprises uveitis, multiple sclerosis, an arthritis, rheumatoid arthritis, osteoarthritis, psoriatic arthritis, spondyloarthriti s, ankylosing spondyliti s, juvenile idiopathic arthritis, neuromyelitis optica, psoriasis, systemic lupus erythematosus, an inflammatory bowel disease, celiac disease, an asthma, allergic asthma, neutrophilic asthma, chronic obstructive pulmonary disease (COPD), scleritis, vasculitis, Behcet's disease, atherosclerosis, atopic dermatitis, emphysema, periodontiti s, allergic rhiniti s, or allograft rejection. 
     
     
       9. The method of  claim 8 , wherein the condition is arthritis. 
     
     
       10. The method of  claim 9 , wherein the arthritis is rheumatoid arthritis, osteoarthritis, psoriatic arthritis, spondyloarthritis, ankylosing spondylitis, or juvenile idiopathic arthritis. 
     
     
       11. A pharmaceutical composition, in the form of a tablet, capsule, or microcapsule, that comprises:
 a therapeutically effective amount of a bacteria strain of genus  Bifidobacterium ; and 
 a pharmaceutically acceptable excipient, diluent, or carrier; 
 wherein the  Bifidobacterium  bacteria strain is lyophilized; 
 wherein the  Bifidobacterium  bacteria strain is positive for fermentation of raffinose as determined by an Analytical Profile Index test comprising:
 (a) contacting a suspension of the  Bifidobacterium  bacteria strain with a Rapid ID 32A strip at 37° C. for at least 4 hours; 
 (b) contacting the suspension with a development reagent comprising FastBlue for at least 5 minutes; and 
 (c) measuring a color of the suspension; and 
 
 wherein the therapeutically effective amount comprises from about 1×10 6  to about 1×10 11  CFU/g of the  Bifidobacterium  bacteria strain with respect to a total weight of the pharmaceutical composition and is sufficient to reduce inflammation caused by Th17 differentiation when administered to a subject. 
 
     
     
       12. The pharmaceutical composition of  claim 11 , wherein the therapeutically effective amount of the  Bifidobacterium  bacteria strain is an amount sufficient to treat a condition mediated by an increase in at least one cytokine in a subject. 
     
     
       13. The pharmaceutical composition of  claim 11 , wherein the  Bifidobacterium  bacteria strain comprises a 16s rRNA gene sequence with at least 95% sequence identity SEQ ID NO:1 as determined by a Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, and a BLOSUM matrix of 62. 
     
     
       14. The pharmaceutical composition of  claim 11 , wherein the  Bifidobacterium  bacteria strain comprises a 16s rRNA gene sequence of SEQ ID NO:1. 
     
     
       15. The pharmaceutical composition of  claim 11 , wherein the  Bifidobacterium  bacteria strain totally or partially colonises an intestine when administered to a subject. 
     
     
       16. The pharmaceutical composition of  claim 11 , wherein a bacterial cell of the  Bifidobacterium  bacteria strain produces an amount of exopolysaccharide that is greater than an amount of the same exopolysaccharide produced by a bacterial cell of  Bifidobacterium breve  strain JCM 7017 as determined by an in vitro assay comprising:
 (i) binding of the exopolysaccharide to Congo Red; and 
 (ii) measuring a light absorbance of the Congo Red bound to the exopolysaccharide for the bacterial cell of the  Bifidobacterium  bacteria strain and the bacterial cell of the  Bifidobacterium  breve strain JCM 7017; and 
 (iii) comparing the light absorbance of the Congo Red bound to the bacterial cell of the  Bifidobacterium  bacteria strain and the bacteria bacterial cell of the  Bifidobacterium breve  strain JCM 7017. 
 
     
     
       17. The pharmaceutical composition of  claim 11 , wherein the pharmaceutical composition further comprises an adjuvant. 
     
     
       18. The method of  claim 1 , wherein an Analytical Profile Index test profile for the  Bifidobacterium  bacteria strain for a-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinose, and mannose is the same as an Analytical Profile Index test profile for a  Bifidobacterium  bacteria strain deposited under accession number NCIMB 42380 for α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinose, and mannose. 
     
     
       19. The pharmaceutical composition of  claim 11 , wherein an Analytical Profile Index test profile for the  Bifidobacterium  bacteria strain for α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinose, and mannose is the same as an Analytical Profile Index test profile for a  Bifidobacterium  bacteria strain deposited under accession number NCIMB 42380 for α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinose, and mannose.